diff options
Diffstat (limited to 'sci-chemistry')
17 files changed, 528 insertions, 182 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 41e7a30fcec2..2eeeb6158656 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index 910723bedde2..fd0cf00cefa4 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,5 +1,5 @@ -DIST chemex-2022.3.5.tar.gz 2845347 BLAKE2B 29b53ba8afcfd91e4f50119f212557de85d8576474b74d2ad925c8c2adb89397640e7b352b6785dc99a8c4e5007294609640219b2374cbb3144f94c5f9113d96 SHA512 3a92702d105e95e0a7b15e01b839d5982df55477afb98e58f7458a0e87230e94597c01d33c219ae469ed62e4ddaecdb787ae435453d428843d5a612159715d2b DIST chemex-2022.3.6.tar.gz 2843118 BLAKE2B e51b385dbf9e3c42f54f95f9929125e3263e12afa62beab8e5b8eb13e78a4fe9a0fb445f4f6c3cd4aa8e71748732ec58124682daa86be079eed036b78492ca71 SHA512 5c734e1b3ea39e9729bada93dfe5bc55f877b69ba6edd9612f95aab0d31949489582957a14f175646c7e6652644a5a55c26bcd74affc7fecc1e7b9cfdd4ceb63 -EBUILD chemex-2022.3.5.ebuild 1250 BLAKE2B d1f61563a971c3c6795b2d398d71073e1db4cc5cca62a6ffc7d9bd2b22b6517417faddc037369fa545fb7f6493d95f658d850c1319eea4adb8bb51c9109e9df7 SHA512 2b1a3a0ca2eeadc7256efadd15a70bdb6b866da1a26a6c209b42fe6e010e871b675f1f2448a2dfdb8fefcbd9c0e97f54ac757a13fb0d29c03bb93ede9c8be97a +DIST chemex-2024.02.16.tar.gz 2756466 BLAKE2B 715499fc3c68079dd66b26a0c4c495029c506be6f009529196fd30a1ec8ff4c0ecbcc4580c9beafd4f3c7df82d6fee525d85c09b031a6dc31d511c1183d30f8d SHA512 7975157b86493c580ce00ef23549597743ff4aa03cebed7d0e0af1d644eed359b5dfa57c51e11f223acebe335d12cb43bd7694a46eeb2ccba70ac6147ba40eda EBUILD chemex-2022.3.6.ebuild 1240 BLAKE2B 46d4f9fd57f5dbc8ad5b527e8568337cd57d3c03f25581d275e15204e5e2ee2c2224c6e8ada71c8d91aed01128be697987cc808bdfd7d7e3abc5f655eb2abb44 SHA512 814348dc6b404698634ecb33ee3956479dd1c05f91f7ca82e4f8a15776a582dd911e30a2070bff727f2aeae678a609fe2d8b676f107741904886c83315dbeb78 +EBUILD chemex-2024.02.16.ebuild 1343 BLAKE2B 1cd03445f8cf230a728b0a0b40ed39ccc11e5ff90b53d6358620a19f9aca2f5d630445bd0a2c9ee1f1dc74e11e5a79740584ace23556bd7ede76959295860868 SHA512 b5a330a8ba2db2f057c7d1cd12de4021e2eb0375474aa8eb0692f8248f448e86354a47e61313b6e37d965447073ed1cb84f300d7ba4e026f8e51f8dd823281a7 MISC metadata.xml 300 BLAKE2B a1ad769918094ddbda13ac92462ec69fa469dfcacde1202c653a4aa7443db661ffa5739cd039b6e38b13f0345a2680f276b4e071362106b162c95cd92007b5a8 SHA512 755c273f6bf67f79c388d06d970702a1d4a9f84338f8d889dd9146905c6994621917952225406ffba5bfe1e1b69f0bfd0f471374178b15343f4927af9de49aef diff --git a/sci-chemistry/chemex/chemex-2022.3.5.ebuild b/sci-chemistry/chemex/chemex-2024.02.16.ebuild index c27017ecebf0..403e48aa069d 100644 --- a/sci-chemistry/chemex/chemex-2022.3.5.ebuild +++ b/sci-chemistry/chemex/chemex-2024.02.16.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_SINGLE_IMPL="yes" -DISTUTILS_USE_PEP517=poetry -PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517=pdm-backend +PYTHON_COMPAT=( python3_{11..12} ) inherit distutils-r1 @@ -14,8 +14,8 @@ HOMEPAGE="https://github.com/gbouvignies/chemex" SRC_URI="https://github.com/gbouvignies/ChemEx/archive/refs/tags/v${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/ChemEx-${PV/_p/-dev}" -SLOT="0" LICENSE="BSD" +SLOT="0" KEYWORDS="~amd64" IUSE="test" @@ -25,18 +25,21 @@ RESTRICT="test" RDEPEND=" $(python_gen_cond_dep ' - >=dev-python/asteval-0.9.25[${PYTHON_USEDEP}] - >=dev-python/cachetools-5.3.0[${PYTHON_USEDEP}] - >=dev-python/lmfit-1.2.0[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.7.1[${PYTHON_USEDEP}] - >=dev-python/numpy-1.24.3[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.10.7[${PYTHON_USEDEP}] - >=dev-python/rapidfuzz-3.0.0[${PYTHON_USEDEP}] - >=dev-python/rich-13.3.4[${PYTHON_USEDEP}] - >=dev-python/scipy-1.10.1[${PYTHON_USEDEP}] + >=dev-python/annotated-types-0.6.0[${PYTHON_USEDEP}] + >=dev-python/cachetools-5.3.2[${PYTHON_USEDEP}] + >=dev-python/emcee-3.1.4[${PYTHON_USEDEP}] + >=dev-python/lmfit-1.2.2[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.8.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1.26.1[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.4.2[${PYTHON_USEDEP}] + >=dev-python/rapidfuzz-3.4.0[${PYTHON_USEDEP}] + >=dev-python/rich-13.6.0[${PYTHON_USEDEP}] + >=dev-python/scipy-1.11.3[${PYTHON_USEDEP}] >=dev-python/tomli-2.0.1[${PYTHON_USEDEP}] ') " DEPEND="${RDEPEND}" distutils_enable_tests pytest + +export PDM_BUILD_SCM_VERSION=${PV} diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index 6eee7db05314..fd6cdbe6dd2c 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -3,12 +3,10 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d -DIST dssp-4.3.1.tar.gz 226842 BLAKE2B 86318f05b8381d94fa9c65a956f5fb607ef8072b0395d912e20697ba36836c449ddff31a4a64d0005bbfe34899f71853c0f15a911042389fc894934c08fc34c8 SHA512 4dc1a3f5c7ba258ebf548674c7b33c36b0e3a7d14911394eb8d2955c235f3cb1d6c50cb03f411db55a8a9d7aa93e4d03354c47f9f0126b0bdcbf40dc9391d403 -DIST dssp-4.4.1.tar.gz 161797 BLAKE2B d6bfb40a730f39e9d5a0988ce22a9dd377ec08a09e29f77e5afaac26d512cf87f6e289c1e4e3e63cfef7354b10fb57bf410bcc169604b1b6a6078380e4f08d26 SHA512 1bcf9e16efc5d3a7de11e24ed63e47d3263123af4670b8f3daa97cdf7cc33202fb4d564acac3024ed4edcce1ef8278f71f5312f27a234d2957afa6f563c88ed6 DIST dssp-4.4.4.1.tar.gz 162809 BLAKE2B 6c3f588a48778cf5f20b40b93736e150a4d366bf44d214b4064362c2a3bce69db415f5d12568a8523d99e2e5a47749d450ff0251dc3035628dbef9343d37e99a SHA512 291810391d74da7ab65bcf4aab61fa4ae1a5518a361fa02d5c15ed0e5c94139fde65e7612a978f5326bd7d93f2ac6ea01b2b65514d6b64f4d062adf112c48deb +DIST dssp-4.4.7.tar.gz 163831 BLAKE2B 195c8fb183df00105098967850b01c0d6acf776f7cfa409fc536c8291e7a467da2adfb5f34d8191e33dbb29bfd254cd414c1b7b76ed3f3b854928c4dc8a5fcdd SHA512 2fe2d8a494b570934c0d28804fe69b6569089ded58ec92bf3d83b25ce60a3b9486490909e187b511328f13498ca9027869e922d95a355cf0e21c2564c2db1b5a EBUILD dssp-2.2.1-r3.ebuild 870 BLAKE2B 9b7542d9ec45b60f5671830e5068e1d1cbcca4b82cf22cc0e2d9804c221f9977cfade439cc6e41a67375b438faca3ffa64fdec23db2b417b58615513fd60ad44 SHA512 964bfd70d98a80e6afd7f28fc6bf7359bbde105e77903211cec04c5adcdce273f1d7142a6d206d644300a1185cba1352bf584499d864809dadad69b2023e50d0 EBUILD dssp-3.0.11.ebuild 875 BLAKE2B 6344416239b93804755b1829dcfcb9e8e461606c217938945bb2fc75e9680f2849b39bdbf0ed361592e703fea493a2dacabca498b26e696c969735a585e5d183 SHA512 353f4f5d7b1b195753c738ecc9fb17b429cdeada757806f5cf9a3da65c6318e3885d2c92fa904d5b3a546756eb87ec90787d158e8a9450b4730dd97b45af970d -EBUILD dssp-4.3.1.ebuild 900 BLAKE2B d99a9024e58e5b2c53cbbfebb662a3fc546dd2a7b16a31394b312a2320bde8df9b62ecdef82295d924141e8427aee56a1e7277132e7767f481041dde6fd7c292 SHA512 1ac6d76fc9c37d5af8eecede2225d86517d27cd96a65ea4a6c9f1ce45eaf2e48fe0772838154639eebdbbccde3dd92bc6f5c9f8b2c37e3c9ca158534e5f8b8fc -EBUILD dssp-4.4.1.ebuild 1327 BLAKE2B 1e84f9fb6e0fa6bf81a3381cd433b7ddcb0e298b5c34f6a8d3007b0a34583e4ea3037b3b1881dab20cb4b0c7c2c9b5e2addca4dd47fa39dba9b992f4c3e140ab SHA512 3bd89956458a91c5f1b56cff97a95b5010904ef1cd1cca591a93be2f5adaf8ad1a6bb5c570dd107a3ff7d78eca9019133b383b2fae1b96a0e70bad5c9f50c97d EBUILD dssp-4.4.4.1.ebuild 1321 BLAKE2B ba06063adc7c9ac9a20c078eeb98c95f0003c5ae58c0db0b5bbb888b194de86e22de9c1549d1911e25e4d5b7a3f99089c0083c281441eeed3dde3ea5e3b8cd14 SHA512 77683bc3bc0aebeb867ffaf94d5f7ce1090f78a73fc739da01c73d3bdab142fc409bce66f85349b627e54376e1279b45a9096a71cac080be10ab0ba4f84d33cb +EBUILD dssp-4.4.7.ebuild 1311 BLAKE2B 6744df1780355e0ac3931c7d87426fc33132db57dbfe6dd237f7df94bb57c3de128f0fa5009391f0b166ce92f0b4e47e8a7f8c1bb2ea492459aeb8f22fdd015a SHA512 dc5ea7e546cb50b2737f0d185cd2f562865319b6bf5d9d1d6ffbdffaa72a4ba2ff9a5d59a37b68798a09b992640b0f57840c896e90641b0f6c02a4bb301cf6a9 MISC metadata.xml 295 BLAKE2B 4355bbe00822cc702acdf70031ab9cd1f2a8f6e076d71016c1783f2a6c052c2da0a1a4a1860062562bb837161787f2481fa6f49c4319c546482a263ebe149bb0 SHA512 ace35ca21c614a7c0cbdea2496be3190a907295053566707c1875836a306cc9e9c96816cca6ce2b514935f6fcd494d2e813f4d94ba88552cd7b86831f30501f4 diff --git a/sci-chemistry/dssp/dssp-4.3.1.ebuild b/sci-chemistry/dssp/dssp-4.3.1.ebuild deleted file mode 100644 index daf7c4f9314d..000000000000 --- a/sci-chemistry/dssp/dssp-4.3.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -inherit cmake - -DESCRIPTION="The protein secondary structure standard" -HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" -SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -BDEPEND=" - dev-libs/boost:=[zlib] - >=dev-libs/libmcfp-1.2.2 - >=sci-libs/libcifpp-5.1.0 -" -DEPEND="" -RDEPEND="${BDEPEND}" - -src_configure() { - # gxrio not packaged - local mycmakeargs=( - -DBUILD_WEBSERVER=OFF - ) - cmake_src_configure -} - -pkg_postinst() { - if has_version "<=sci-chemistry/gromacs-2022"; then - ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" - ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" - ewarn - ewarn "Feel free to mask newer versions if needed." - fi -} diff --git a/sci-chemistry/dssp/dssp-4.4.1.ebuild b/sci-chemistry/dssp/dssp-4.4.7.ebuild index d79883c4e211..cebac1ce3a1a 100644 --- a/sci-chemistry/dssp/dssp-4.4.1.ebuild +++ b/sci-chemistry/dssp/dssp-4.4.7.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -18,14 +18,13 @@ KEYWORDS="~amd64 ~x86" CDEPEND=" dev-libs/boost:=[zlib] >=dev-libs/libmcfp-1.2.2 - >=sci-libs/libcifpp-5.1.0 + >=sci-libs/libcifpp-7.0.3 " BDEPEND="${CDEPEND}" # doc? ( # || ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc ) # dev-python/weasyprint # ) -DEPEND="" RDEPEND="${CDEPEND}" #src_prepare() { @@ -38,8 +37,8 @@ RDEPEND="${CDEPEND}" src_configure() { local mycmakeargs=( - #-DGENERATE_DOCUMENTATION=$(usex doc) - -DGENERATE_DOCUMENTATION=NO + #-DBUILD_DOCUMENTATION=$(usex doc) + -DBUILD_DOCUMENTATION=NO ) cmake_src_configure } diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 71f6bb8fd082..05fca2bd57ec 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -7,18 +7,21 @@ DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 2dc1b15ca8692ca5cf4ad1c7a266b9e2ced0 DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1eba42850916e7cb70ef459a8d9c6ebc8c1bbe3c105f5b23161dd5c552ec00505d7c0036649b782cf52c311498743 SHA512 91217394f534ca8f78f73189059712e1c2cd354b658722f23768b12748f7bfaf1a5e95227c5ed1b69c1a9b72c3174e9600a712c157ea2f27156387efb823dd67 DIST gromacs-2023.4.tar.gz 42044149 BLAKE2B 2c13a04ddbfc167a7887d44bb6fdacde4ece4e8cf2ba920f453fc6150423c3cae39cd1afe0eebb52b9fbc72fe37fee527c83227a0f3fe21b289655b5c1cd29c5 SHA512 7913348d0da25e095b795123894f4e2007f66cf2455664edeb7bc1edc09f2e0da9911bc9501e3001278ab59917ccef838c485e6b6533c1c816c54c6dbd56350c DIST gromacs-2024.1.tar.gz 42324773 BLAKE2B 6600c802c39bf7c36d8e388ced202504dcceb3ec018d5f48af4f55e43dd170157a9b6335ce1b20a73623d05a391787936c2ab6ee48ab031d17078256eb7153c5 SHA512 fea88fac28ec142201eec1cea984eabd9db43346254ac555954a13fdbae5a5b00281a17efc8dba8ab0ac42794e3cce41b314c5cb36fb4292a1c6d2668b2ba192 +DIST gromacs-2024.2.tar.gz 42367929 BLAKE2B 3ffdbc075c3b92d1200376b45b0599eafc15454830f0a5b1c1e250a50d8fcd16a6a904c5f04979328b1afc89e6c77b15df44d9c240425507bafe0689107bf9a0 SHA512 aa6c0ae3849d6e58ae43ffef6ef90d06f62e53ab70047c643c90e9f3ac7305c2d52bb5c9da02b174a6244e8a6adfb6d205d1c9d22312709a1b358923f5d10741 DIST gromacs-2024.tar.gz 42455653 BLAKE2B 86446c5e95f9ddaf718126c409389730ee1642f36c3e0d844eb4b3a640c275e7979581365dacb57ac66daec296bbd94be6d5c0376f7255d3d3950f6759f8d69a SHA512 d64bf3cbe579003ce37dfd3d27c68746a04360d9d5491c638f3f2bd9af2c938504b0c9710c62e85225370ddf5418e6ebc2422033e46af5eee6e4aaa53699fed7 DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6 DIST manual-2021.7.pdf 12256526 BLAKE2B 6f298d7dac142f66914bbc2ea7d6ca70c4aeafaf33ccf12336d5cec64b1f1097b5332c767bb411ccef706ec6184479a84bcf59bda21c4249d45d8ce3dea08e79 SHA512 197765accb8ab6c5f1cc94b2697ff1817e157d85fa231dfe36a85036076e04da2a8035de66aba4f46c6dd7f553176357b94c92e1da5d1dabc574c627deee5279 DIST manual-2022.6.pdf 13081140 BLAKE2B 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index 000000000000..a3319899d419 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2024.2.ebuild @@ -0,0 +1,335 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_OPTIONAL=1 +DISTUTILS_USE_PEP517=no +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + " + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + # since 2022 arm support was dropped (but not arm64) + KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="https://www.gromacs.org/" + +# see COPYING for details +# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0= ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi[cxx] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) + build-manual? ( + app-text/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] + ') + media-gfx/mscgen + media-gfx/graphviz + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + doc? ( !build-manual ) + cuda? ( single-precision ) + opencl? ( single-precision ) + cuda? ( !opencl ) + clang-cuda? ( clang cuda ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp + python-single-r1_pkg_setup +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + + cmake_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + if use build-manual; then + # try to create policy for imagemagik + mkdir -p "${HOME}"/.config/ImageMagick + cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF + fi +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + local acce="AUTO" + + if use custom-cflags; then + #go from slowest to fastest acceleration + acce="None" + if (use amd64 || use x86); then + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + use cpu_flags_x86_avx512f && acce="AVX_512" + elif (use arm); then + use cpu_flags_arm_neon && acce="ARM_NEON" + elif (use arm64); then + use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" + fi + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_USE_LMFIT=EXTERNAL + -DGMX_USE_MUPARSER=EXTERNAL + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local gpu=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + local mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=$(usex mpi) + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${gpu[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use build-manual; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use build-manual; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + + if use doc; then + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" + fi + fi + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"/usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/articles.html" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest index 330cfa72107a..07dd49e6424d 100644 --- a/sci-chemistry/modeller/Manifest +++ b/sci-chemistry/modeller/Manifest @@ -1,3 +1,4 @@ -DIST modeller-9.25.tar.gz 44820658 BLAKE2B b3e8a3cc8cc70689a25bc5ed2eee294d67bef8eea9ed4b64d41aba3a27c0bc428ae58e74d734da0eaab7e4fabb213d098b9ba66b9569557159ac7d4a58244b0a SHA512 93f273aba0ec0f884cde5bbcc24769a09386bfc6bf1744d80001e41924b1a682225ba3c554fb9898ef3bfd1fd8451f9458bb92431b20f2f51b01781e79686c91 -EBUILD modeller-9.25.ebuild 3838 BLAKE2B 43569c6712ed8b26152784fdedadb440014b934517b23d9f0b7d3005313767a81e9ce9de85a8d23f7407ed2d44efab69a8d4fea15739a9e89e6cfd51a2a106b4 SHA512 bb8e488420677dbbf1e8f14ef490896d46378099e7c8b6d3faa3eb44c9dc44ed4dff765ec82ae032f1dcea47b7cedcb7299759bd53bb6e4b090cc2d8eace72c2 +AUX modeller-10.5-fix-except.patch 1494 BLAKE2B 111205f2a20df7e473340ff96d5dfd428a1e1a3edccebcb6ccf51ae9c96be28950bc7433c5ae45165b66e0ce3f8213ea4554f65036dbce783b544fad3035982b SHA512 923be1e727327321930ac9893f041bfa85079da8e1e646e79ea2efdd36581f49498ef05b55a812b06f85bf8bcccd7d5d98c98be2d5ad7a3908313daef5ef5ad6 +DIST modeller-10.5.tar.gz 38272541 BLAKE2B 9c71a9f1e4c34c91852db73ebf86f71cf355217d6889566ff6840dc6874d4906b989a36f3dd642ba4e4d1fe671c1a15753a33e7fabb53adc9182c76fe4fdb6c4 SHA512 666c5367a14084438c96b68ba0779ebd97ca831a4a6538f66e54b63657c8e13b85931c2de8300311f1df7d02907b2ec61f27f95b0704f2c6a313b6baee56febc +EBUILD modeller-10.5.ebuild 3754 BLAKE2B 31ba39d295194c676b52a0999834d1ef7dbd09e62086deda48941ed023345a557dc859e384062d10ebee9dc15b22f10ffdf68c9794bc575f389da3588d0b08c9 SHA512 402464996c584d6b648e0961a77072ba02b7a167a178441f9247b99fce0c92dd6428ae62f330f44f36739d0ef2e16ac6d773e1f4484913dbd4cc058c99f1c4e6 MISC metadata.xml 375 BLAKE2B 949d039d3cd24da52efe20f58e7da07b4371e90ef72f314d076110b4604af1c0b7a77c1241172cf5e0a1c40363a00728d14d6faf30af73d27317f24d5a6c2289 SHA512 52791b3cb6a3998676f23e16346b9c4f447f42de8a58e612eebdf8ebfd34bc724c4994c3accebf00d552187bc80d1c097f73bd02b6fd6874a84441627eb785ca diff --git a/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch b/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch new file mode 100644 index 000000000000..f480a8229bf9 --- /dev/null +++ b/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch @@ -0,0 +1,29 @@ +--- a/modlib/modeller/top_interpreter/__init__.py 2024-03-27 15:52:04.005550025 +0300 ++++ b/modlib/modeller/top_interpreter/__init__.py 2024-03-27 15:54:00.776897686 +0300 +@@ -65,7 +65,7 @@ + if len(line) > 0: + try: + self._parse_top_ini_line(line.split(None, 4), vars) +- except TypeError, detail: # noqa: E999 ++ except (TypeError, detail): # noqa: E999 + mod_log_write("read_top__E> " + str(detail)) + mod_log_write(" top.ini line: " + line) + raise +@@ -115,7 +115,7 @@ + try: + fh = self._open_include_file( + self.variables['include_file']) +- except IOError, detail: ++ except (IOError, detail): + mod_log_write("runlines__E> " + str(detail)) + mod_log_write(" TOP Command line: " + line) + raise +@@ -162,7 +162,7 @@ + indxca = self._run_top_cmd(cmd, indxca, lines, callstack, + subrout) + _modeller.mod_top_post() +- except (IndexError, SyntaxError, TypeError), detail: ++ except (IndexError, SyntaxError, TypeError, detail): + mod_log_write("runlines__E> " + str(detail)) + mod_log_write(" TOP Command line: " + line) + raise diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-10.5.ebuild index 1401279be237..80718ec876c8 100644 --- a/sci-chemistry/modeller/modeller-9.25.ebuild +++ b/sci-chemistry/modeller/modeller-10.5.ebuild @@ -1,10 +1,11 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python3_{9..10} ) -DISTUTILS_USE_SETUPTOOLS=no +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 inherit distutils-r1 @@ -13,14 +14,15 @@ HOMEPAGE="https://salilab.org/modeller/" SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz" LICENSE="modeller" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="doc examples" -SLOT="0" RESTRICT="mirror" DEPEND=">=dev-lang/swig-1.3" -RDEPEND="" + +PATCHES=( "${FILESDIR}/${P}-fix-except.patch" ) INPATH="${EPREFIX}"/opt/modeller${ver} @@ -40,8 +42,6 @@ pkg_setup() { python_prepare_all() { sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die rm -rf modlib/modeller/python_library || die - sed -i '1 i\#!/usr/bin/python' bin/modslave.py || die - 2to3 -w -n modlib/modeller || die distutils-r1_python_prepare_all } @@ -77,7 +77,6 @@ python_install_all() { exeinto ${INPATH}/bin doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh - python_foreach_impl python_doscript bin/modslave.py dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest index c89726c20774..5fdb76ae39ea 100644 --- a/sci-chemistry/molmol/Manifest +++ b/sci-chemistry/molmol/Manifest @@ -1,6 +1,8 @@ +AUX molmol-2k_p2-gcc14-fix.patch 357 BLAKE2B e7c1692e7a45ed2b83c38fa8b7ffe1a563f752660f3e2dc2098eb1de4491cd8919190d04cdc9d31f036b42a8fda6d6200fa347dfc7aed0fa46d75e1e3103e6cb SHA512 6138806de3222b073ce0f77c2c6d7060cbc9e3ba729553f61b93e44c671008da0e1ce64bc6fc0d9293dba203d71ae76cff1bea698e03a42d3e5a5901e6e8ccc0 DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287 DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97 EBUILD molmol-2k_p2-r8.ebuild 2284 BLAKE2B fa9954fca3dd8b52450beb1c0901abc71743672d7a76e2daa2bb05f52280ecf7dec5c401da24ce3e72f429cb69b27738117e33d41b49a96836b1b407efef67f0 SHA512 d813743572479b5eb0ed4181d42743402c4bd0a5a8e012f32bad03c4be68f38329722b749abc91845ba9c25642b19f5e2c4b5578ed9d3f7d03beaabbaa3345f5 +EBUILD molmol-2k_p2-r9.ebuild 2314 BLAKE2B f54b8793c88c3e5d14a128e922d9d22dcc5ad861c76a205b84a0a4d8f36ccdf8e6259955e71257689424ac48819fcd3350105e4472202681e8a9bc80c43d9d21 SHA512 56e0839d1f3d971d549c2bcde64115b17e3b7adccaf63b75e7221247684c7b7ee40df89d30c2b0d0acd28aa4e147523644f34ce496cf6a9e51ff540616123bda MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch b/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch new file mode 100644 index 000000000000..7041ced28efe --- /dev/null +++ b/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch @@ -0,0 +1,12 @@ +Bug: https://bugs.gentoo.org/923325 +--- a/src/motogl/MotOGLDump.c ++++ b/src/motogl/MotOGLDump.c +@@ -245,7 +245,7 @@ jpegErrHand(j_common_ptr jpegInfoP) + + #ifdef PNG_SUPPORT + static void +-pngErrHand(png_structp pngStrucP, char *errMsg) ++pngErrHand(png_structp pngStrucP, const char *errMsg) + { + IORaiseError(errMsg); + longjmp(png_jmpbuf(pngStrucP), 1); diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild new file mode 100644 index 000000000000..29769cede153 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild @@ -0,0 +1,103 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit desktop toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" + +# Original page dead +#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +HOMEPAGE=" + http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html + http://pjf.net/science/molmol.html +" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2 + https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png +" +S="${WORKDIR}" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + || ( + ( + media-libs/mesa[X(+)] + x11-libs/libGLw + ) + media-libs/mesa[motif(-),X(+)] + ) + media-libs/libjpeg-turbo:= + media-libs/libpng:= + media-libs/tiff:= + sys-libs/zlib + virtual/glu + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-gcc14-fix.patch +) + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" + MAKEOPTS="${MAKEOPTS} -j1" #880621 +} + +src_prepare() { + default + + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff + + eapply "${WORKDIR}"/patches/ldflags.patch + eapply "${WORKDIR}"/patches/opengl.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s|ksh|sh|" \ + -e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\"|" \ + -i "${S}"/molmol || die + sed \ + -e "s|^MCFLAGS.*|MCFLAGS = ${CFLAGS}|" \ + -e "s|^CC.*|CC = $(tc-getCC)|" \ + -i "${S}"/makedef || die + + eapply "${WORKDIR}"/patches/cast.patch + eapply -p0 "${WORKDIR}"/patches/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + eapply "${WORKDIR}"/patches/${P}-fink.patch + + eapply "${WORKDIR}"/patches/wild.patch + tc-export AR +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + doexe src/main/molmol + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + make_desktop_entry "${PN}" MOLMOL + newicon "${DISTDIR}/${PN}_256.png" "${PN}.png" + + einstalldocs + dodoc HISTORY +} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 27ab37bd4be7..dbc27f448a0d 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,6 +1,5 @@ AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c -DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91 -EBUILD pymol-2.5.0-r3.ebuild 2617 BLAKE2B d79d2bcdbb284b0eb6bb3eb4863288aaaebfa94c65b3d9205e60caf607195fd7631b7b29cc7a27ff25b25f4236ea211b99b96dbafe084042b4a0d20c613edb05 SHA512 4ec711441b124b5abc0a062dac1293385dfecf83db6c1c7380907d2ae680f4a064cbb08260bd2b058741764dd25be1570e8fbb402c3204da58f08bf7efd48678 -EBUILD pymol-2.5.0-r4.ebuild 2826 BLAKE2B 3a5a557058ff0f552e3160c8a127bdbfd257d1fc47530b4cc79b0ac5751b3a2959822c8562aca0d66aafa4c3e48a287784e0b968c3c9cbdc6fa980db49768735 SHA512 1f219a9ea5ee7946626c15bfb3e0e01501bf16dd08c1763bd986a6766e0cce92846c3ac9ed9e1e88fa19467b35a0d21b67ef0c58dbd81bd002968f609f802e78 +DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2 +EBUILD pymol-3.0.0.ebuild 2831 BLAKE2B b277127a25bc4b292238b374bd6945e372bbdfc6a7855a3e03c7855dd49fb2c75f3b064fbeb783f6dfc838f3069aeb65139a23caecc858c6557eed34a40cd79e SHA512 890933535af6f7bb0f49b554e6f9ab5fc2134a04c163ef28c61e2fb351faa5fd3c5aa166dd8bc444d649dd5688f1c5a2579acfdaeca41b8ca3f1247f24027351 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild deleted file mode 100644 index ae7eda57d7a6..000000000000 --- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild +++ /dev/null @@ -1,100 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_EXT=1 - -inherit desktop flag-o-matic xdg distutils-r1 - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz - " -LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991 -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="+netcdf web" - -DEPEND=" - dev-cpp/msgpack-cxx - dev-libs/mmtf-cpp - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pmw[${PYTHON_USEDEP}] - media-libs/freetype:2 - media-libs/glew:0= - media-libs/glm - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - netcdf? ( sci-libs/netcdf:0= ) -" -RDEPEND="${DEPEND} - sci-chemistry/chemical-mime-data -" - -S="${WORKDIR}"/${PN}-open-source-${PV} - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -i setup.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.py || die - sed \ - -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ - -i setup.py || die - - append-cxxflags -std=c++0x - - distutils-r1_python_prepare_all -} - -python_configure_all() { - use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - python_doscript "${T}"/${PN} -} - -python_install_all() { - distutils-r1_python_install_all - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF || die - PYMOL_PATH="${EPREFIX}/usr/share/pymol" - PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" - PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" - EOF - - doenvd "${T}"/20pymol - - newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry "${PN} %u" PyMol ${PN} \ - "Graphics;Education;Science;Chemistry;" \ - "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" - - if ! use web; then - rm -rf "${D}/$(python_get_sitedir)/web" || die - fi - - rm -f "${ED}"/usr/share/${PN}/LICENSE || die -} diff --git a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild index e4b4d3e2eadb..150f7732d930 100644 --- a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild +++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{9..12} ) DISTUTILS_USE_PEP517="setuptools" DISTUTILS_EXT=1 @@ -15,7 +15,10 @@ SRC_URI=" https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz " -LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991 + +S="${WORKDIR}"/${PN}-open-source-${PV} + +LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" IUSE="+netcdf web" @@ -39,8 +42,6 @@ RDEPEND="${DEPEND} sci-chemistry/chemical-mime-data " -S="${WORKDIR}"/${PN}-open-source-${PV} - PATCHES=( "${FILESDIR}/${PN}-2.5.0-format-security.patch" ) @@ -59,7 +60,7 @@ python_prepare_all() { -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ -i setup.py || die - append-cxxflags -std=c++0x + append-cxxflags -std=c++17 distutils-r1_python_prepare_all } |